HOOMD-Blue

http://codeblue.umich.edu/hoomd-blue/about.html

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HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many processor cores on a fast cluster.

Object-oriented design patterns are used in HOOMD-blue so it versatile and expandable. Various types of potentials, integration methods and file formats are currently supported, and more are added with each release. The code is available and open source, so anyone can write a plugin or change the source to add additional functionality.

Simulations are configured and run using simple python scripts, allowing complete control over the force field choice, integrator, all parameters, how many time steps are run, etc... . The scripting system is designed to be as simple as possible to the non-programmer.

The HOOMD-blue development effort is led by the Glotzer group at the University of Michigan. Many groups from different universities have contributed code that is now part of the HOOMD-blue main package, see the credits page for the full list.

• • Executes particle dynamics simulations fast on NVIDIA GPUs

  • Supports Linux and Mac OS X

  • Pair Potentials - cutoff

    • • CGCMM

      • DPD (dissipative particle dynamics)

      • EAM (embedded atom method)

      • Gaussian

      • Lennard-Jones

      • Morse

      • User-specified (tabulated)

      • Shifted Lennard-Jones

      • Yukawa

  • Pair Potentials - long range

    • • PPPM Electrostatics

  • Bond Potentials

    • • FENE

      • Harmonic

  • Angle Potentials

    • • Harmonic

      • CGCMM

  • Dihedral/Improper Potentials

    • • Harmonic

  • Wall Potentials

    • • Lennard-Jones

  • Constraint forces

• • • Constrain selected particles to the surface of a sphere

• • Integrators

    • • Berendsen NVT

      • Brownian dynamics NVT, on free particles and rigid bodies

      • NPT, on free particles or rigid bodies

      • NVE, on free particles and rigid bodies

      • NVT, on free particles and rigid bodies

  • Energy minimization

    • • FIRE

  • Dump file formats

    • • HOOMD-blue's XML input format

      • MOL2

      • DCD

      • PDB

  • Simple and powerful python script interface for defining simulations

• • • Specify any combination of potentials, integrators, etc...

    • Compute and set parameters

    • Read and write particle properties during a simulation

    • Read and write bond topology during a simulation

    • Specify initial conditions within a job script

• • Performs 2D and 3D simulations

  • Advanced built-in initial configuration generators

  • Human readable XML input files

  • Space-filling curve particle reordering to increase performance

  • Extensible object-oriented design. Additional features may be added in new classes contained in plugins.

  • Simulations can be visualized in real-time using VMD's IMD interface.

  • Pair potentials and forces may be varied smoothly to 0 at the cutoff

  • Real time analysis may be run at a non-linear rate

  • Temperature, pressure, and box size can be varied smoothly over a run

  • Flexible selection of particles for integration